key: cord-318181-xxc7vdnt
authors: Ahmed, Anwar E.; Al-Jahdali, Hamdan; Alshukairi, Abeer N.; Alaqeel, Mody; Siddiq, Salma S.; Alsaab, Hanan; Sakr, Ezzeldin A.; Alyahya, Hamed A.; Alandonisi, Munzir M.; Subedar, Alaa T.; Aloudah, Nouf M.; Baharoon, Salim; Alsalamah, Majid A.; Al Johani, Sameera; Alghamdi, Mohammed G.
title: Early identification of pneumonia patients at increased risk of Middle East respiratory syndrome coronavirus infection in Saudi Arabia
date: 2018-03-14
journal: Int J Infect Dis
DOI: 10.1016/j.ijid.2018.03.005
sha: 
doc_id: 318181
cord_uid: xxc7vdnt

BACKGROUND: The rapid and accurate identification of individuals who are at high risk of Middle East respiratory syndrome coronavirus (MERS-CoV) infection remains a major challenge for the medical and scientific communities. The aim of this study was to develop and validate a risk prediction model for the screening of suspected cases of MERS-CoV infection in patients who have developed pneumonia. METHODS: A two-center, retrospective case–control study was performed. A total of 360 patients with confirmed pneumonia who were evaluated for MERS-CoV infection by real-time reverse transcription polymerase chain reaction (rRT-PCR) between September 1, 2012 and June 1, 2016 at King Abdulaziz Medical City in Riyadh and King Fahad General Hospital in Jeddah, were included. According to the rRT-PCR results, 135 patients were positive for MERS-CoV and 225 were negative. Demographic characteristics, clinical presentations, and radiological and laboratory findings were collected for each subject. RESULTS: A risk prediction model to identify pneumonia patients at increased risk of MERS-CoV was developed. The model included male sex, contact with a sick patient or camel, diabetes, severe illness, low white blood cell (WBC) count, low alanine aminotransferase (ALT), and high aspartate aminotransferase (AST). The model performed well in predicting MERS-CoV infection (area under the receiver operating characteristics curves (AUC) 0.8162), on internal validation (AUC 0.8037), and on a goodness-of-fit test (p = 0.592). The risk prediction model, which produced an optimal probability cut-off of 0.33, had a sensitivity of 0.716 and specificity of 0.783. CONCLUSIONS: This study provides a simple, practical, and valid algorithm to identify pneumonia patients at increased risk of MERS-CoV infection. This risk prediction model could be useful for the early identification of patients at the highest risk of MERS-CoV infection. Further validation of the prediction model on a large prospective cohort of representative patients with pneumonia is necessary.

Middle East respiratory syndrome coronavirus (MERS-CoV) was first identified in Saudi Arabia in 2012. The diagnosis of this infection remains complex (Al Johani and Hajeer, 2016; Sung et al., 2016; Ahmed, 2017a) and it has a high fatality rate (Ahmed, 2017b, c; Aleanizy et al., 2017; Sherbini et al., 2017; Kim et al., 2017) . The early detection and identification of individuals at high risk of a disease is the most effective strategy to improve patient clinical outcomes (Ahmed, 2017a) and reduce the costs of testing, both physical and economic (Ahmed et al., 2011 (Ahmed et al., , 2013 . The real-time reverse transcription polymerase chain reaction (rRT-PCR) has been found to be valid and accurate for the evaluation of respiratory swabs, sputum, and other endotracheal aspirate material (Corman et al., 2012a, b) . However, although rRT-PCR is the most accurate and sensitive test available at the authors' centers, absolute identification of MERS-CoV may require multiple clinical specimens from different sources and take days (Corman et al., 2012a, b; Anon, 2018a) .

The Saudi Ministry of Health (MOH) has developed MERS-CoV visual triage guidelines to identify suspected cases (Anon, 2018b) . The current guidelines include fever, respiratory symptoms, gastrointestinal symptoms, chronic diseases, and risk of exposure to MERS-CoV. In clinical practice, identifying high-risk individuals can be challenging, since most laboratory-confirmed MERS-CoV patients report common clinical risk indices to patients with other respiratory conditions. For instance, respiratory and gastrointestinal symptoms are common for both MERS-CoV and non-MERS-CoV patients (Mohd et al., 2016) . Thus, further exploration must take place to reduce the risk of MERS-CoV infection. A risk prediction model is urgently needed to stratify patients with suspected MERS-CoV. This may decrease the risk of virus transmission to others who are in close contact, for example healthcare workers, patients, and hospital visitors, by allowing the careful management of those who are potentially infected at an early stage of infection. Developing a MERS-CoV prediction model may more efficiently aid physicians in identifying individuals at high risk and selecting the necessary test(s) to improve prevention and control measures.

Several methodological studies have shown that combining demographic characteristics with clinical, radiological, and laboratory information can improve risk assessment and diagnostic accuracy (Ahmed et al., 2011 (Ahmed et al., , 2013 Sidransky, 2002; Etzioni et al., 2003) . These previous studies used a linear combination to develop an algorithm that combines demographic characteristics, symptoms, and clinical, radiological, and laboratory findings to identify the highly suspected MERS-CoV cases.

MERS-CoV was initially identified in a patient being treated for pneumonia in 2012 (Zaki et al., 2012) , and since then, pneumonia and its symptoms have remained common characteristics in MERS-CoV patients (Saad et al., 2014; Choi et al., 2016) .

The aim of this study was to develop and validate a reliable risk prediction model for the screening of suspected cases of MERS-CoV infection in patients who have developed pneumonia.

A two-center, retrospective case-control study was conducted utilizing data from King Abdulaziz Medical City in Riyadh (KAMC-R) and King Fahad General Hospital in Jeddah (KFGH-JED), Saudi Arabia. The data were obtained between September 1, 2012 and June 1, 2016. KFGH-JED experienced a MERS outbreak between March and May 2014 (Oboho et al., 2015) , and KAMC-R experienced a large MERS outbreak between June and August 2015 (Al-Dorzi et al., 2016) . Both study centers applied the Saudi MOH case definitions (Anon, 2018b) to identify suspected individuals in the population studied, and rRT-PCR was used as the gold standard test to diagnose MERS-CoV in multiple and different clinical specimens when necessary. MERS-CoV-related symptoms were common at both centers.

The project received ethical approval from two independent ethics committees: the Saudi MOH (IRB log number 16-230E) and King Abdullah International Medical Research Center (study number RC17/061), Riyadh Saudi Arabia.

During the study, the medical records of 829 subjects who were being assessed by rRT-PCR for suspected MERS-CoV were reviewed. The suspicion of MERS-CoV infection at both KAMC-R and KFGH-JED was determined based on the Saudi MOH guidelines (Anon, 2018b) . Two groups were compared: patients who were positive and patients who were negative for MERS-CoV infection. In an effort to reduce heterogeneity between the study groups, only subjects with a lung infiltrate on chest X-ray and/or computed tomography (CT) scan of the chest were included in the analysis. Thus, subjects who had no available results of a chest X-ray or CT scan of the chest were excluded. The initial screening for suspected MERS-CoV patients includes pneumonia (Anon, 2018b) . Most of the patients studied were evaluated for pneumonia immediately after presentation.

The study excluded subjects who were less than 15 years of age (pediatrics/children), as defined in the Saudi MOH guidelines (Anon, 2018b) , and excluded subjects who had upper respiratory tract infections (respiratory symptoms, positive or negative MERS-CoV rRT-PCR, and normal chest X-ray and CT scan of the chest).

The final sample comprised a cohort of 360 subjects who had a lung infiltrate on chest X-ray and/or a CT scan of the chest, who were classified according to the results of MERS-CoV rRT-PCR. The case group consisted of 135 pneumonia patients who were positive for MERS-CoV infection, and the control group consisted of 225 pneumonia patients who were negative for MERS-CoV infection.

Cases were defined as patients with MERS-CoV pneumonia who had positive MERS-CoV rRT-PCR on nasopharyngeal aspirate and/ or bronchoalveolar lavage in addition to a lung infiltrate on chest Xray and/or CT scan of the chest. Controls were defined as patients with respiratory symptoms, a lung infiltrate on chest X-ray and/or CT scan of the chest, pneumonia, and negative MERS-CoV rRT-PCR result of nasopharyngeal aspirate and/or bronchoalveolar lavage.

Nineteen predictive variables were included: age, sex, fever (temperature !38 C), one composite respiratory symptom (the presence of cough, bloody cough, shortness of breath, or chest pain), one composite gastrointestinal symptoms (the presence of diarrhea, vomiting, or nausea), seven MERS-CoV potential risk factors (contact with sick patients or camels, severe illness (defined according to the patient's clinical status, 'yes/no', which is based on clinical judgment), diabetes, lung disease, liver disease, renal disease, and heart disease), and seven laboratory measurements (white blood cell (WBC) count (Â10 9 /l), platelets (Â10 9 /l), creatinine (mmol/l), bilirubin (mmol/l), alanine aminotransferase (ALT; U/l), aspartate aminotransferase (AST; U/l), and albumin (g/ l)). The reference ranges for the laboratory measures were as follows: WBC count, 4-11 Â10 9 /l; platelets, 150-400 Â 10 9 /l; creatinine, 50-98 mmol/l; bilirubin, 3.4-20.5 mmol/l; ALT, 5-55 U/l; AST, 5-34 U/l; albumin, 35-55 g/l. No serological tests were available at the centers for these patients.

Stata statistical software release 15, 2017 (StataCorp. LLC, College Station, TX, USA) was used for the data analysis. The sample characteristics were recorded as the frequency and percentage, or as the mean AE standard deviation (SD). Laboratory measurements were summarized as the median and 25th-75th percentiles. A subgroup analysis (Chi-square test, independent samples t-test, or Mann-Whitney U-test) was used to identify unadjusted associations between demographic, clinical, and laboratory measurements according to MERS-CoV status. The performance of each bivariate predictor was further assessed by unbiased estimate, the area under the curve (AUC), and its 95% confidence interval (CI).

Stepwise binary logistic regression was employed to develop a MERS-CoV risk prediction model and identify factors that could be used to estimate the probabilities of MERS-CoV infection.

The goodness-of-fit of the final model was tested by Hosmer-Lemeshow procedure: a large p-value indicates that a model has a good fit. The discrimination ability between high and minimal risk of MERS-CoV infection of the final model was assessed by the AUC and its 95% CI. A receiver operating characteristics (ROC) curve was generated for the risk prediction model. Two hundred random samples were drawn with replacements from the original study sample (N = 360). The model internal validity was assessed in these 200 samples by the AUC and its 95% CI. Optimal cut-off values of the probabilities for each model were determined using a generalized Youden index (Youden, 1950) . At these thresholds, it was possible to achieve the best balance between specificity and sensitivity.

A total of 360 pneumonia patients were included in the analysis: 37.5% were confirmed MERS-CoV-positive and 62.5% were confirmed MERS-CoV-negative. The mean age at presentation was 55.9 years, with a standard deviation of 20.2 years; age ranged between 16 and 109 years. Of the total sample, 6.9% had been in contact with a sick patient or camel, 60% had fever, 84.2% had at least one respiratory symptom, and 18.6% had at least one gastrointestinal symptom. The two groups were similar in the distribution of age (p = 0.220) and sex (p = 0.079). The characteristics of the sample can be found in Table 1 .

Subgroup analyses are presented in Tables 1 and 2. The Chisquare test or the independent samples t-test revealed that sex (p = 0.079) and age (p = 0.220) were similar in the two groups. The risk of MERS-CoV infection was similar in patients with and without fever (p = 0.267), respiratory symptoms (p = 0.080), or gastrointestinal symptoms (p = 0.382). Severe illness (p = 0.001), contact with a sick patient or camel (p = 0.001), diabetes (p = 0.001), heart disease (p = 0.007), and renal disease (p = 0.025) were significantly associated with an increased risk of MERS-CoV infection.

The independent samples Mann-Whitney U-test revealed that the WBC count (p = 0.001) and platelet count (p = 0.006) were significantly lower in patients who were positive for MERS-CoV than in those who were negative for MERS-CoV infection. In contrast, creatinine (p = 0.001), bilirubin (p = 0.001), AST (p = 0.001), and albumin (p = 0.004) were significantly higher in patients who were positive for MERS-CoV than in those who were negative for MERS-CoV infection. ALT (p = 0.352) was insignificantly higher in patients who were positive for MERS-CoV than in those who were negative for MERS-CoV infection.

According to the individual ROC curve analysis (Table 3) , severe illness, diabetes, WBC count, creatinine, bilirubin, albumin, and AST were the most important predictors of MERS-CoV infection.

A risk prediction model was developed using stepwise binary logistic regression (p 0.05). The model retained seven independent variables that were associated with increased odds of MERS-CoV (Table 4 ). Male sex (adjusted odds ratio (aOR) 1.883, p = 0.043), contact with a sick patient or camel (aOR 21.915, p = 0.001), diabetes (aOR 2.703, p = 0.002), severe illness (aOR 6.312, p = 0.001), low WBC count (aOR 0.897, p = 0.001), high AST (aOR 1.007, p = 0.007), and low ALT (aOR 0.995, p = 0.024) were found to have a significant impact on the prediction of MERS-CoV.

The Hosmer-Lemeshow test indicated that this model fitted the data well (p = 0.592). This model showed substantial discrimination, with an AUC of 0.8162 and a 95% CI of 0.7651-0.8674 ( Figure  1 ). The prediction model was validated using the bootstrap procedure. A total of 200 random samples were drawn with replacements from the original sample, and the model showed a substantial ability to assess MERS-CoV infection in this study population (AUC 0.804, 95% CI 0.7838-0.8235).

The findings in Table 4 were used to create a risk-probability model. The risk prediction for the model can be expressed by the following equation: predicted probability = [1 + exp(1.409-(0.633 Â male) À (3.087 Â sick patient or camel contact) À (0.995 Â diabetes) À (1.842 Â severe illness) + (0.109 Â WBC count) À (0.007 Â AST) + (0.005 Â ALT))] À1 . A calculator was developed to calculate the potential risk of MERS-CoV infection in pneumonia patients.

We determined the optimal cut-off or threshold values of the probabilities to mark the differences between the high-risk and low-risk groups. When an equal weight was given for sensitivity and specificity (m = 1), the optimal cut-off value (probability !0.33) produced sensitivity and specificity of 0.716 and 0.783, respectively. When more weight was given for sensitivity than specificity (m = 0.50), the optimal cut-off value (probability !0.20) produced sensitivity and specificity of 0.902 and 0.550, respectively. When more weight was given for specificity than sensitivity (m = 1.50), the optimal cut-off value (probability !0.39) produced sensitivity and specificity of 0.647 and 0.831, respectively.

Based on data from the two largest hospitals in Saudi Arabia, a risk prediction model was developed for MERS-CoV infection in pneumonia patients. This model was generated from a retrospective study and should be assessed prospectively for external validation. Seven variables were identified as having a great impact on the MERS-CoV risk assessment prediction. The risk prediction model highlights the strong potential impact of male sex, contact with a sick patient or camel, severe illness, diabetes, low WBC count, high AST, and low ALT on MERS-CoV infection. These few important parameters could be part of routine medical examinations to be performed (for the purpose of identifying highly suspected individuals) in daily clinical practice in order to make a prompt and timely clinical decision. According to the model, high AST was associated with an increased risk of being infected with MERS-CoV. This finding is similar to that of Mohd et al., who noted high AST levels in MERS-CoV patients (Mohd et al., 2016) . Unlike their findings, it was noted in the present study that the impact of ALT became significantly negative after controlling for several confounders. However, this type of association should be evaluated further in a prospective study in the presence of other unmeasured confounders.

Although sex was found to have no impact on MERS-CoV infection in the unadjusted analysis, the multivariate analysis revealed that the risk of MERS-CoV infection was 88.3% times higher in males than in females. This may be because other factors are playing a role in the development of MERS-CoV in males, such as camel contact, since males are more likely than females to have contact with camels.

In agreement with the recent Saudi MOH MERS-CoV visual triage guidelines for the identification of suspected cases (Anon, 2018b) , it was found that the odds of being infected with MERS-CoV were higher in patients with diabetes as compared to those with no diabetes. This also supports the findings of previous studies (Badawi and Ryoo, 2016; Assiri et al., 2013; Al-Tawfiq et al., 2014; Alraddadi et al., 2016) in which researchers systematically recognized that diabetes is a risk factor for MERS-CoV infection.

These findings indicate that more attention should be given to assessing the risk of MERS-CoV infection in diabetic patients and whether the risk depends on a specific diabetes type or condition in these patients. As asserted in the Saudi MOH MERS-CoV visual triage guidelines and many other studies (Muhairi et al., 2016; Younan et al., 2016; Reeves et al., 2015; Sabir et al., 2016; Azhar et al., 2014a, b) , contact with a sick patient or camel was identified as an independent predictor of MERS-CoV infection, according to the risk prediction model. It must be noted that the finding in the present study could have been limited by combining camel contact and sick patient contact due to the small sample size of each category.

This study shows the importance of incorporating various types of information to improve the performance of the risk prediction. According to the linear combination model, it was found that several of the parameters highlighted in the Saudi MOH MERS-CoV visual triage guidelines were not able to distinguish between 'highrisk' and 'low-risk' groups, nor did they help in predicting MERS-CoV infection. For instance, fever, respiratory symptoms, gastrointestinal symptoms, heart disease, and renal disease were noted to have an insignificant impact on MERS-CoV infection.

However, in agreement with the Saudi MOH MERS-CoV guidelines and two other reports (Mohd et al., 2016; Arabi et al., 2017) , the odds of being infected with MERS-CoV were associated with a significant risk reduction of 10.3% for each unit increase in WBC count.

These results suggest that demographic, clinical, radiological, and laboratory data should be used in routine practice to identify suspected MERS-CoV cases, as such data could serve as the first line of prevention strategies. It was found that the accuracy of prediction (Figure 1 ) was further improved when combining various medical and patient variables as opposed to relying on a single factor (Table 3 ). This has been proven theoretically and in application (Ahmed et al., 2013 (Ahmed et al., , 2011 (Ahmed et al., , 2015 Etzioni et al., 2003; Shen, 2008; Pepe and Thompson, 2000; Su and Liu, 1993; Thompson, 2003) , where a linear combination has been used to maximize the diagnostic accuracy of a disease of interest.

The strength of this study lies in the fact that a simple and applicable predictive model was developed that incorporates demographic, clinical, radiological, and laboratory data, where these were functionally associated and contributed greatly to stratifying and distinguishing between a high and a minimal risk of MERS-CoV infection. This simple evaluation of suspected MERS-CoV cases appears promising and could be implemented easily in routine clinical practice. This model could be used as a risk stratification method or a triage tool to help physicians in making an informed decision and planning the next step when deciding whether an rRT-PCR or further investigation is necessary.

It was possible to derive a risk probability algorithm (range 0-1), a generalized Youden index (Choi et al., 2016) was used to determine an optimal cut-off to stratify the risk, and a risk probability of !0.41 was identified as being the optimal cut-off, with a sensitivity of 0.688 and specificity of 0.789.

Several limitations to the proposed risk prediction model were identified. The study findings were based on a retrospective design; therefore this prediction model should be interpreted with caution. Limited information was available on patient variables, clinical variables, and transmission routes. For example, information on primary cases and secondary cases may be supplemented by the results of clinical, radiological, and laboratory data. In this study, 'contact with a sick patient' and 'contact with a sick camel' were combined into one variable due to the small number in each category. Severe illness was based on a subjective judgment. An additional potential limitation was that the duration of symptoms was not available for these patients. This study investigated a very specific population (pneumonia) at only two centers, which could compromise the applicability and generalizability of the risk prediction model. Moreover, the prediction model may not be generalizable to patients who do not fulfill the MOH guidelines. Further validation of the prediction model on an external sample and prospective cohort of representative patients with pneumonia is necessary, specifically in relevant settings: emergency, outpatient, inpatient, and community.

Despite these limitations, the model developed shows promise for the identification of suspected MERS-CoV cases in clinical practice. This model could be applicable in various healthcare settingsinpatient, outpatient, and emergency departmentsbecause no extensive laboratory testing is required and samples may be available within short turnaround times. This may allow rapid evaluation and improve clinical decision-making.

In conclusion, this study provides a simple, practical, and valid algorithm to identify individuals at increased risk of MERS-CoV infection among patients who have developed pneumonia. This risk model is not only useful for risk stratification and decisionmaking in clinical practice, but it could also be useful in preventing and managing the possible spread of MERS-CoV. The usefulness of this newly developed tool most be validated in an external prospective study.

The project received ethical approval from two independent ethics committees: the Saudi Ministry of Health (IRB log number 16-230E) and King Abdullah International Medical Research Center (study number RC17/061), Riyadh Saudi Arabia.

None.

None declared. 

Accuracy and cost comparison in medical testing using sequential testing strategies

Reducing cost in sequential testing: a limit of indifference approach

Believe the extreme (BE) strategy at the optimal point: what strategy will it become

Diagnostic delays in 537 symptomatic cases of Middle East respiratory syndrome coronavirus infection in Saudi Arabia

Estimating survival rates in MERS-CoV patients 14 and 45 days after experiencing symptoms and determining the differences in survival rates by demographic data, disease characteristics and regions: a worldwide study

The predictors of 3-and 30-day mortality in 660 MERS-CoV patients

MERS-CoV diagnosis: an update

The critical care response to a hospital outbreak of Middle East respiratory syndrome coronavirus (MERS-CoV) infection: an observational study

Middle East respiratory syndrome coronavirus: a case-control study of hospitalized patients

Outbreak of Middle East respiratory syndrome coronavirus in Saudi Arabia: a retrospective study

Risk factors for primary Middle East respiratory syndrome coronavirus illness in humans

Laboratory testing for Middle East respiratory syndrome coronavirus (MERS-CoV)

Case definition and surveillance guidance -updated

Critically ill patients with the Middle East respiratory syndrome: a multicenter retrospective cohort study

Epidemiological, demographic, and clinical characteristics of 47 cases of Middle East respiratory syndrome coronavirus disease from Saudi Arabia: a descriptive study

Detection of the Middle East respiratory syndrome coronavirus genome in an air sample originating from a camel barn owned by an infected patient

Evidence for camel-to-human transmission of MERS coronavirus

Prevalence of comorbidities in the Middle East respiratory syndrome coronavirus (MERS-CoV): a systematic review and meta-analysis

Clinical presentation and outcomes of Middle East Respiratory Syndrome in the Republic of Korea

Assays for laboratory confirmation of novel human coronavirus (hCoV-EMC) infections

Detection of a novel human coronavirus by real-time reverse-transcription polymerase chain reaction

Combining biomarkers to detect disease with application to prostate cancer

Middle East respiratory syndrome coronavirus (MERS-CoV) outbreak in South Korea, 2015: epidemiology, characteristics and public health implications

Predictors of MERS-CoV infection: a large case control study of patients presenting with ILI at a MERS-CoV referral hospital in Saudi Arabia

Epidemiological investigation of Middle East respiratory syndrome coronavirus in dromedary camel farms linked with human infection in Abu Dhabi Emirate

MERS-CoV outbreak in Jeddah-a link to health care facilities

Combining diagnostic test results to increase accuracy

MERS-CoV geography and ecology in the Middle East: analyses of reported camel exposures and a preliminary risk map

Clinical aspects and outcomes of 70 patients with Middle East respiratory syndrome coronavirus infection: a single-center experience in Saudi Arabia

Co-circulation of three camel coronavirus species and recombination of MERS-CoVs in Saudi Arabia

On the principles of believe the positive and believe the negative for diagnosis using two continuous tests

Middle East respiratory syndrome coronavirus in Al-Madinah City, Saudi Arabia: Demographic, clinical and survival data

Emerging molecular markers of cancer

Linear combinations of multiple diagnostic markers

Comparative evaluation of three homogenization methods for isolating Middle East respiratory syndrome coronavirus nucleic acids from sputum samples for real-time reverse transcription PCR

Assessing the diagnostic accuracy of a sequence of tests

Index for rating diagnostic tests

MERS and the dromedary camel trade between Africa and the Middle East

Isolation of a novel coronavirus from a man with pneumonia in Saudi Arabia

The authors acknowledge the Saudi Ministry of Health and King Abdullah International Medical Research Center for approving this research project. The authors would like to thank the leaders of King Abdulaziz Medical City in Riyadh and King Fahad General Hospital in Jeddah for their support and understanding.

Supplementary data associated with this article can be found, in the online version, at https://doi.org/10.1016/j.ijid.2018.03.005.
